diff README.rst @ 0:f411ce97a351 draft

Uploaded initial version 1.0.2-2

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+CEAS: Cis-regulatory Element Annotation System
+==============================================
+
+Galaxy tool wrapper for the CEAS (Cis-regulatory Element Annotation System), which
+can be used to annotate intervals and scores with genome features.
+
+This tool uses the Cistrome version of the package, which provides two versions of
+the core program: in addition to the ``ceas`` program (the same as that available
+from the main CEAS website), it also includes the ``ceasBW`` program (which can handle
+bigwig input).
+
+The tool assumes that the ``ceas`` and ``ceasBW`` programs are on the Galaxy user's
+path.
+
+The official CEAS website is at:
+
+- http://liulab.dfci.harvard.edu/CEAS/index.html
+
+The Cistrome version can be found via
+
+- https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
+and the CEAS programs, and setting the appropriate environment variables.
+
+In addition this will also install a data manager which can be used to install
+reference GDB data files necessary for the tool.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``ceas_wrapper.xml`` (the Galaxy tool definition)
+- ``ceas_wrapper.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/ceas/`` folder. You will then
+need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
+by adding the line:
+
+    <tool file="ceas/ceasbw_wrapper.xml" />
+
+You also need to make a copy of the ``ceas.loc`` file (a sample version is
+provided here) which points to the available GDB files for different genomes.
+
+This file should be placed in the ``tool-data`` directory of your Galaxy
+installation.
+
+Reference Data
+==============
+
+CEAS requires reference data in the form of GDB files (essentially, SQLite database
+files) containing the RefSeq genes for the genome in question.
+
+A limited number of GDB files are available for download from the CEAS website; to
+make new ones, see the section "Build a sqlite3 file with a gene annotation table
+and genome background annotation for CEAS" in the CEAS manual:
+
+- http://liulab.dfci.harvard.edu/CEAS/usermanual.html
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+1.0.2-2    - Major updates to fix various bugs, add tests and enable ceasBW to
+             be used without an existing chromosome sizes file.
+1.0.2-1    - Modified to work with Cistrome-version of CEAS (includes additional
+             'ceasBW' program which can take bigWig input)
+1.0.2-0    - Initial version.
+========== ======================================================================
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/ceas
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_ceas.sh`` script.